Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017535.1 Corchorus olitorius cultivar O-4 contig17568, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 9625
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:8 original size:3 final size:3

Alignment explanation


    Indices: 1--48  Score: 96
    Period size: 3  Copynumber: 16.0  Consensus size: 3

                                                                           
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

         49 AATATCAGAT


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   45  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:1109 original size:2 final size:2

Alignment explanation


    Indices: 1102--1148  Score: 76
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       1092 TCGAATCCTC

                                                                       *   
       1102 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TG TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA

                 
       1145 TA TA
          1 TA TA

       1149 GTAATGATTC


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   2   40  0.95
   3    2  0.05

ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:4199 original size:14 final size:15

Alignment explanation


    Indices: 4175--4203  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       4165 TTTAGAATGG

                           
       4175 GAAGAAAGAAGAAGA
          1 GAAGAAAGAAGAAGA

                           
       4190 GAAG-AAGAAGAAGA
          1 GAAGAAAGAAGAAGA

       4204 AAAAGTGTCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (15 bp):   
GAAGAAAGAAGAAGA

Found at i:6439 original size:15 final size:15

Alignment explanation


    Indices: 6421--6470  Score: 50
    Period size: 13  Copynumber: 3.4  Consensus size: 15

       6411 TTATAGCTAG

                           
       6421 TTATTATATATGTAA
          1 TTATTATATATGTAA

                       *   
       6436 TTA-TA-ATATATAA
          1 TTATTATATATGTAA

            *               
       6449 CTAGTTATATATGTAA
          1 TTA-TTATATATGTAA

             *    
       6465 TAATTA
          1 TTATTA

       6471 ATTATGTTAA


Statistics
Matches: 27,  Mismatches: 5, Indels: 6
        0.71            0.13        0.16

Matches are distributed among these distances:
  13    9  0.33
  14    2  0.07
  15    8  0.30
  16    8  0.30

ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48


Consensus pattern (15 bp):   
TTATTATATATGTAA

Found at i:9589 original size:2 final size:2

Alignment explanation


    Indices: 9582--9611  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       9572 ATCTTAATTA

                                                        
       9582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9612 CTCGACATCT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.